The GST bill should come up in the middle or end of the remainder of the budget session and should be passed then. The Finance Minister has already said he expects it to be passed by the end of the budget session because the composition of the Rajya Sabha will change slightly in the government's favour.
The Aadhar bill was made a money bill leveraging the government's majority in the Lok Sabha and the rule that the Speaker has to certify whether the bill is a money bill or not; and her ruling cannot be questioned.

To be completely honest, I had not expected a lot from the first half of the budget session and in the beginning it seemed that was the case. But the speed and alacrity with which the opposition has facilitated the passage of bills towards the end of the session suggests they too are realizing that disruption is a strategy with diminishing returns.
That said, The opposition still has the legitimate instrument of referring bills to standing committees for deeper study. That is what it will follow in the RS. But overall, mostly hits, and few misses.

Let us see this in perspective.
It is only with constitutional amendment bills such as GST that the government has a serious Rajya Sabha problem. With normal bills that require just 50 per cent majority, it has a variety of instruments at its disposal - asking 'friendly' opposition parties to stay away from the house, thus bringing down the threshold of passing percentage; getting some parties to abstain in return for other favours; etc.
Remember the Coal mining ordinance? How hard Piyush Goel worked to convince opposition parties that the ordinance would be in their favour? You had the BJP make speeches that argued against the ordinance and the government - but end up supporting the ordinance so it got cleared. Those kinds of strategies depend entirely on the skills of the government... how it deploys them.

I am not sure what the threshold should be - there are big differences even within the government (viz the views of CEA and the actual provisions in the bill ) But the government will not be allowed to ram through something that is not popular - and it realizes that as well.

I think there is I-can-outstare-you game going on. I don't think there is any serious difficulty in forming the government - just that Mehbooba has to display her 'extreme' reluctance in forming a government with the BJP.
Trust me, the option is staying in government is better than allowing the government to collapse leading to President's Rule and elections....

I HOPE the government doesn't use this route - it undermines democracy, politics and in some ways, shows the inefficiency of the government. After all, in the past too, governments with majority in the lower house but not in the upper house have passed legislation and it has been with the consent or disagreement of the opposition in the upper house.
You are right, it was a way to show up the opposition - hope it doesn't happen too often.

Will the implementation of the seventh Pay Commission be a smart move by the government to win back confidence and boost its political clout, especially in the wake of assembly elections across various states?

Well, the implementation of the 7th Pay Commission is not a matter of choice but a compulsion. And frankly, awards of this kind are now taken for granted by employees.
I think what is much more important is the record of governance of the state governments and what else the centre can come up with to woo the poor - because ultimately it is the poor that stand between victory and defeat for any government. Which is why the PM is repeating the vikas mantra....